One of the hardest challenges in medical genetics is to reach a molecular diagnosis in the presence of rare brain disorders. Hereditary spinocerebellar ataxia (HA), characterized by high clinical and genetic heterogeneity, is among the diseases that present this challenge. HA can have features overlapping with those of other neurological diseases, especially hereditary spastic paraplegia (HSP), as routine clinical application of next generation sequencing (NGS) has confirmed. This article reviews different NGS methods applied in heterogeneous cohorts of patients with suspected HA and suggests that exome sequencing should be considered the first-tier genetic approach in this setting. Its application lends support to the hypothesis of HA and HSP as two extremes of a continuous spectrum.